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The Northern Appalachian / Acadian ecoregion is as well known for its aquatic features as for its mountains and coast. With snowy winters and humid summers, the once glaciated region boasts over 18,000 miles of streams and over 14,000 lakes. Split by the Appalachian mountains, large scale patterns of freshwater diversity correspond to huge drainage basins, the North Atlantic draining south and the St. Lawrence draining north, which have internally similar climatic and historical freshwater linkages. A portion of a third, the Lake Ontario basin, drains west from the Tug Hill plateau in New York (Figure 1).

The North Atlantic Major Drainage Basin: Draining southward, this basin cover half of the ecoregion (81% of the U.S.) and is noted for high quality temperate coastal rivers, numerous lakes, and significant runs of anadromous fish such as Atlantic salmon, shad, and herring. Endangered aquatic fauna include the dwarf wedge and brook floater mussels, Atlantic and shortnose sturgeons and the ringed boghaunter dragonfly. Major rivers include the St. John, St. Croix, Penobscot, Kennebec, Androscoggin, the upper portions and headwaters of the Connecticut, Hudson and Merrimack and the Medway, St. Marys, and other southerly draining smaller coastal rivers of Nova Scotia.

The St. Lawrence Major Drainage Basin: Draining northward from the mountains to the St Lawrence River, this half of the region (21% of the U.S. portion) has a more cold tolerant fauna and lower freshwater species richness than the North Atlantic drainage (Abell et al. 2002). It is known for numerous lakes including Lake Champlain, Lac Saint-Jean, and Lake Manicouagan, and their large tributaries such as the Missisquoi, Lamoile, Winooski, Otter, Ausable, and Great Chazy along with other rivers draining northwest out of the Adirondacks such as the St. Regis, Raquette, Grass, Osweegatchie, and Indian. Significant self-sustaining runs of anadromous Atlantic salmon occur in the Canadian portion of the basin, which also includes the Upper Saint-Francois, Chaudiere, Rimouski, Matane, Casapedia, and Saint-Jean in Quebec and the Nepisiguit and Miramichi Rivers in New Brunswick.

The Ontario Major Drainage Basin: A small part of the New York Tug Hill region defined by the watershed of Lake Ontario, this basin includes the headwaters of the Black, Saimon-Sanity and Oneida Rivers.

Within the major drainage basins, 12 large watershed units, termed ecological drainage units (EDUs) were defined by ecologists based on faunal and geomorphic similarities and used for coarse level freshwater stratification of the region (Figure 2). Note that some, e.g. Merrimack and Middle Connecticut, cover only a small portion of the ecoregion.